Clonal plants, like cyanobacteria, are widespread and perform important ecosystem functions, influencing the structure and composition of the habitats in which they occur. Some cyanobacteria perform biological nitrogen fixation (BNF) and can affect plant growth as nitrogen (N) is a limiting nutrient. Therefore, to investigate whether heterocystous cyanobacteria favour individual growth and reproductive strategies (sexual reproduction and clonal growth) of Salvinia auriculata, we carried out a greenhouse experiment with the inoculation of two strains of cyanobacteria, Desmonostoc (UFLA 12) and Cronbergia (UFLA 35). S. auriculata ramets were grown in plastic pots with the following treatments: (D) Desmonostoc (UFLA 12) inoculum; (C) Cronbergia (UFLA 35) inoculum; (D + C) Cronbergia (UFLA 35) + Desmonostoc (UFLA 12) inoculum, and (Co) control, absence of cyanobacteria. Treatments (D) and (D + C) positively influenced the clonal growth of S. auriculata. Desmonostoc inoculation contributed to numerical increase in shoots, biomass gain, and shoot size. Cronbergia (UFLA 35) alone was not able to promote the growth of S. auriculata, only in consortium with Desmonostoc (UFLA 12). We conclude that the inoculation of Desmonostoc (UFLA 12) and Cronbergia (UFLA 35) favours the clonal growth of S. auriculata contributing to its more vigorous spread. The fact that Desmonostoc (UFLA 12) and Cronbergia (UFLA 35) favoured the clonal growth of S. auriculata may serve as a tool to assist in understanding the excessive growth of these plants in aquatic environments, for acting as a potential biofertiliser.